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. 2023 Mar 16:2023:gigabyte78.
doi: 10.46471/gigabyte.78. eCollection 2023.

Genome assembly of the deep-sea coral Lophelia pertusa

Santiago Herrera  1 , Erik E Cordes  2
Affiliations

Genome assembly of the deep-sea coral Lophelia pertusa

Santiago Herrera et al. GigaByte. .

Abstract

Like their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly of Lophelia pertusa from the southeastern coast of the USA, the first one for a deep-sea scleractinian coral species. We generated PacBio continuous long reads data for an initial assembly and proximity ligation data for scaffolding. The assembly was annotated using evidence from transcripts, proteins, and ab initio gene model predictions. This assembly is comparable to high-quality reference genomes from shallow-water scleractinian corals. The assembly comprises 2,858 scaffolds (N50 1.6 Mbp) and has a size of 556.9 Mbp. Approximately 57% of the genome comprises repetitive elements and 34% of coding DNA. We predicted 41,089 genes, including 91.1% of complete metazoan orthologs. This assembly will facilitate investigations into the ecology of this species and the evolution of deep-sea corals.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1.
Figure 1.
In situ images of the coral Lophelia pertusa in the Atlantic USA southeast shelf. (a) Lophelia reef. (b) Close-up of Lophelia polyps. (c) Collection of the Lophelia sample sequenced in this study using the hydraulic arm of the remotely operated vehicle (ROV) Jason. (d) Lophelia sample being placed in ROV Jason’s biobox. Images (a) and (b) courtesy of NOAA OER, Windows to the Deep 2019. Images (c) and (d) courtesy of the Deep SEARCH program and copyright Woods Hole Oceanographic Institution.
Figure 2.
Figure 2.
Flow chart depicting the assembly pipeline for the Lophelia pertusa genome. Dotted boxes indicate the different de novo assemblies. Letters indicate the designed nomenclature of each assembly as reflected in the text and Table 1. Data inputs are indicated in maroon font. Software packages are highlighted with blue background.
Figure 3.
Figure 3.
Quality metrics for the final Lophelia pertusa genome assembly (I), compared to other reference genome assemblies of scleractinian corals. BUSCO percentages indicate the proportion of the 954 metazoan orthologs that are complete and single-copy (S), complete and duplicated (D), fragmented (F), and missing (M). The phylogeny shown on the left is the best-scoring maximum likelihood tree inferred from single-copy orthologs. All branches had 100% bootstrap confidence.
See this image and copyright information in PMC

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